There's quite a few good anime sci-fi franchises. Gundam's already been mentioned, here's a few more:
Macross/Robotech-A transforming alien ship commandeered by humans stands against a force of giant aliens, and they use transforming fighter planes and music to stop them. Sounds corny, but it is actually well executed. Macross is the original Japanese series and has spawned multiple sequels, some of which are available in the US while some aren't. Robotech, which was a translated form of Macross in the 80s, was melded with two other anime series and given a seperate continuity of sorts. It's complicated
Neon Genesis Evangelion-Apocalyptic series which revolutionized the mecha genre. Mentally unstable pilots battle mysterious 'angels'-bizzare monsters-who threathen Tokyo, but there's a lot more going on than meets the eye.
Cowboy Bebop-Or, if giant robots aren't your thing, there's this, a series which possibly influenced Firefly.